[2024-01-24 11:35:22,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:22,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:22,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg54b3edc6-b748-47b0-8ffc-cb54d73f32b8/dqc_reference
[2024-01-24 11:35:26,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,241] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg39943979-d5ba-4ab6-ac77-bff5577bc2b8/GCF_019093865.1_ASM1909386v1_genomic.fna.gz | prodigal -d GCF_019093865.1_ASM1909386v1_genomic.fna/cds.fna -a GCF_019093865.1_ASM1909386v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:33,926] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:33,927] [INFO] Task started: HMMsearch
[2024-01-24 11:35:33,927] [INFO] Running command: hmmsearch --tblout GCF_019093865.1_ASM1909386v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54b3edc6-b748-47b0-8ffc-cb54d73f32b8/dqc_reference/reference_markers.hmm GCF_019093865.1_ASM1909386v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:34,268] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:34,269] [INFO] Found 6/6 markers.
[2024-01-24 11:35:34,301] [INFO] Query marker FASTA was written to GCF_019093865.1_ASM1909386v1_genomic.fna/markers.fasta
[2024-01-24 11:35:34,302] [INFO] Task started: Blastn
[2024-01-24 11:35:34,302] [INFO] Running command: blastn -query GCF_019093865.1_ASM1909386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54b3edc6-b748-47b0-8ffc-cb54d73f32b8/dqc_reference/reference_markers.fasta -out GCF_019093865.1_ASM1909386v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:34,899] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:34,903] [INFO] Selected 27 target genomes.
[2024-01-24 11:35:34,904] [INFO] Target genome list was writen to GCF_019093865.1_ASM1909386v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:34,936] [INFO] Task started: fastANI
[2024-01-24 11:35:34,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg39943979-d5ba-4ab6-ac77-bff5577bc2b8/GCF_019093865.1_ASM1909386v1_genomic.fna.gz --refList GCF_019093865.1_ASM1909386v1_genomic.fna/target_genomes.txt --output GCF_019093865.1_ASM1909386v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:50,135] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:50,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54b3edc6-b748-47b0-8ffc-cb54d73f32b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:50,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54b3edc6-b748-47b0-8ffc-cb54d73f32b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:50,147] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:50,147] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:50,147] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Lentibacillus saliphilus	strain=YIM 93176	GCA_019093865.1	2737028	2737028	type	True	100.0	1061	1063	95	conclusive
Virgibacillus halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	76.87	80	1063	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	76.7328	71	1063	95	below_threshold
Lentibacillus halodurans	strain=CGMCC 1.3702	GCA_900112045.1	237679	237679	type	True	76.6198	66	1063	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	76.5998	67	1063	95	below_threshold
Oceanobacillus kimchii	strain=X50	GCA_000340475.1	746691	746691	type	True	76.5064	59	1063	95	below_threshold
Oceanobacillus rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	76.3317	68	1063	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	76.3238	86	1063	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	76.2009	50	1063	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	76.1726	89	1063	95	below_threshold
Oceanobacillus alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	76.146	51	1063	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:50,149] [INFO] DFAST Taxonomy check result was written to GCF_019093865.1_ASM1909386v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:50,149] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:50,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:50,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54b3edc6-b748-47b0-8ffc-cb54d73f32b8/dqc_reference/checkm_data
[2024-01-24 11:35:50,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:50,183] [INFO] Task started: CheckM
[2024-01-24 11:35:50,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019093865.1_ASM1909386v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019093865.1_ASM1909386v1_genomic.fna/checkm_input GCF_019093865.1_ASM1909386v1_genomic.fna/checkm_result
[2024-01-24 11:36:19,566] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:19,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:19,591] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:19,591] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:19,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019093865.1_ASM1909386v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:19,592] [INFO] Task started: Blastn
[2024-01-24 11:36:19,592] [INFO] Running command: blastn -query GCF_019093865.1_ASM1909386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54b3edc6-b748-47b0-8ffc-cb54d73f32b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_019093865.1_ASM1909386v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:20,345] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:20,350] [INFO] Selected 27 target genomes.
[2024-01-24 11:36:20,350] [INFO] Target genome list was writen to GCF_019093865.1_ASM1909386v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:20,369] [INFO] Task started: fastANI
[2024-01-24 11:36:20,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg39943979-d5ba-4ab6-ac77-bff5577bc2b8/GCF_019093865.1_ASM1909386v1_genomic.fna.gz --refList GCF_019093865.1_ASM1909386v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019093865.1_ASM1909386v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:36,457] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:36,478] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:36,479] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_019093865.1	s__Lentibacillus_B saliphilus	100.0	1061	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009741735.1	s__Lentibacillus_B sp009741735	77.5464	211	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900162695.1	s__Lentibacillus siamensis	77.1903	72	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310895.1	s__Virgibacillus halodenitrificans	76.866	79	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	98.29	98.21	0.89	0.88	7	-
GCF_016919725.1	s__Virgibacillus sp016919725	76.7775	89	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCF_009728145.1	s__Ornithinibacillus caprae	76.7614	86	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176885.1	s__Oceanobacillus senegalensis	76.7013	72	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000724085.1	s__Virgibacillus manasiensis	76.6244	71	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112045.1	s__Lentibacillus halodurans	76.5888	67	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013373365.1	s__Lentibacillus sp013373365	76.5752	59	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018333235.1	s__Ornithinibacillus bavariensis	76.5684	70	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	98.72	98.72	0.93	0.93	2	-
GCF_000482485.1	s__Ornithinibacillus globulus	76.5195	73	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908155.1	s__Oceanobacillus caeni	76.5048	55	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.65	98.42	0.88	0.86	14	-
GCF_001659985.1	s__Oceanobacillus sp001659985	76.4112	53	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873675.1	s__Lentibacillus litoralis	76.3291	87	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002153375.1	s__Oceanobacillus rekensis	76.3042	69	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577245.1	s__Ornithinibacillus sp000577245	76.2925	72	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110695.1	s__Lentibacillus subterraneus	76.1801	90	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
GCF_016908325.1	s__Aquibacillus albus	76.1523	50	1063	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:36,480] [INFO] GTDB search result was written to GCF_019093865.1_ASM1909386v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:36,481] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:36,487] [INFO] DFAST_QC result json was written to GCF_019093865.1_ASM1909386v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:36,488] [INFO] DFAST_QC completed!
[2024-01-24 11:36:36,488] [INFO] Total running time: 0h1m14s